5hd9

Crystal Structure of the N-terminal domain of the DNA packaging ATPase from bacteriophage phi29Crystal Structure of the N-terminal domain of the DNA packaging ATPase from bacteriophage phi29

Structural highlights

5hd9 is a 1 chain structure with sequence from Bacillus virus phi29. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.941Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PKG16_BPPH2 ATPase required for the genome encapsidation reaction. Part of the active packaging motor via the binding to the packaging RNA (pRNA), itself fixed to the head-tail connector at the unique portal vertex of the prohead. Binds and supercoils the DNA-gp3 to produce an initiation complex for DNA packaging. Provides the energy to actively pump the viral DNA into the prohead. Approximately one molecule of ATP is used in the packaging of 2 bp of viral DNA. After packaging, the ATPase and the pRNA are released from the prohead.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Ring NTPases are a class of ubiquitous molecular motors involved in basic biological partitioning processes. dsDNA viruses encode ring ATPases that translocate their genomes to near-crystalline densities within pre-assembled viral capsids. Here, X-ray crystallography, cryoEM, and biochemical analyses of the dsDNA packaging motor in bacteriophage phi29 show how individual subunits are arranged in a pentameric ATPase ring and suggest how their activities are coordinated to translocate dsDNA. The resulting pseudo-atomic structure of the motor and accompanying functional analyses show how ATP is bound in the ATPase active site; identify two DNA contacts, including a potential DNA translocating loop; demonstrate that a trans-acting arginine finger is involved in coordinating hydrolysis around the ring; and suggest a functional coupling between the arginine finger and the DNA translocating loop. The ability to visualize the motor in action illuminates how the different motor components interact with each other and with their DNA substrate.

Structural and Molecular Basis for Coordination in a Viral DNA Packaging Motor.,Mao H, Saha M, Reyes-Aldrete E, Sherman MB, Woodson M, Atz R, Grimes S, Jardine PJ, Morais MC Cell Rep. 2016 Mar 1;14(8):2017-29. doi: 10.1016/j.celrep.2016.01.058. Epub 2016 , Feb 18. PMID:26904950^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Simpson AA, Tao Y, Leiman PG, Badasso MO, He Y, Jardine PJ, Olson NH, Morais MC, Grimes S, Anderson DL, Baker TS, Rossmann MG. Structure of the bacteriophage phi29 DNA packaging motor. Nature. 2000 Dec 7;408(6813):745-50. PMID:11130079 doi:10.1038/35047129
↑ Koti JS, Morais MC, Rajagopal R, Owen BA, McMurray CT, Anderson DL. DNA packaging motor assembly intermediate of bacteriophage phi29. J Mol Biol. 2008 Sep 19;381(5):1114-32. doi: 10.1016/j.jmb.2008.04.034. Epub 2008, Apr 20. PMID:18674782 doi:http://dx.doi.org/10.1016/j.jmb.2008.04.034
↑ Guo P, Peterson C, Anderson D. Prohead and DNA-gp3-dependent ATPase activity of the DNA packaging protein gp16 of bacteriophage phi 29. J Mol Biol. 1987 Sep 20;197(2):229-36. doi: 10.1016/0022-2836(87)90121-5. PMID:2960820 doi:http://dx.doi.org/10.1016/0022-2836(87)90121-5
↑ Garvey KJ, Saedi MS, Ito J. The complete sequence of Bacillus phage phi 29 gene 16: a protein required for the genome encapsidation reaction. Gene. 1985;40(2-3):311-6. PMID:3879485
↑ Mao H, Saha M, Reyes-Aldrete E, Sherman MB, Woodson M, Atz R, Grimes S, Jardine PJ, Morais MC. Structural and Molecular Basis for Coordination in a Viral DNA Packaging Motor. Cell Rep. 2016 Mar 1;14(8):2017-29. doi: 10.1016/j.celrep.2016.01.058. Epub 2016 , Feb 18. PMID:26904950 doi:http://dx.doi.org/10.1016/j.celrep.2016.01.058

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OCA

[1] Simpson AA, Tao Y, Leiman PG, Badasso MO, He Y, Jardine PJ, Olson NH, Morais MC, Grimes S, Anderson DL, Baker TS, Rossmann MG. Structure of the bacteriophage phi29 DNA packaging motor. Nature. 2000 Dec 7;408(6813):745-50. PMID:11130079 doi:10.1038/35047129

[2] Koti JS, Morais MC, Rajagopal R, Owen BA, McMurray CT, Anderson DL. DNA packaging motor assembly intermediate of bacteriophage phi29. J Mol Biol. 2008 Sep 19;381(5):1114-32. doi: 10.1016/j.jmb.2008.04.034. Epub 2008, Apr 20. PMID:18674782 doi:http://dx.doi.org/10.1016/j.jmb.2008.04.034

[3] Guo P, Peterson C, Anderson D. Prohead and DNA-gp3-dependent ATPase activity of the DNA packaging protein gp16 of bacteriophage phi 29. J Mol Biol. 1987 Sep 20;197(2):229-36. doi: 10.1016/0022-2836(87)90121-5. PMID:2960820 doi:http://dx.doi.org/10.1016/0022-2836(87)90121-5

[4] Garvey KJ, Saedi MS, Ito J. The complete sequence of Bacillus phage phi 29 gene 16: a protein required for the genome encapsidation reaction. Gene. 1985;40(2-3):311-6. PMID:3879485

[5] Mao H, Saha M, Reyes-Aldrete E, Sherman MB, Woodson M, Atz R, Grimes S, Jardine PJ, Morais MC. Structural and Molecular Basis for Coordination in a Viral DNA Packaging Motor. Cell Rep. 2016 Mar 1;14(8):2017-29. doi: 10.1016/j.celrep.2016.01.058. Epub 2016 , Feb 18. PMID:26904950 doi:http://dx.doi.org/10.1016/j.celrep.2016.01.058

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